In April 1963 the Historic Peace Church Council of Canada, a Canada-wide inter-Mennonite peace organization, called a meeting of all existing inter-Mennonite peace, relief, and service agencies, as well as representatives of all Mennonite and Brethren in Christ conferences. Out of this meeting came the decision to form a national inter-Mennonite body that would unite all Canadian Mennonite groups in all the activities they wished to do together. MCCC was born in December 1963 in Winnipeg.

MCCC became the most comprehensive of Canadian Mennonite and Brethren in Christ organizations. The MCCC board included representatives from 11 Mennonite and Brethren in Christ groups. The organization was given a broad mandate to work in the areas of peace education, relief and development, voluntary service, immigration, government contacts (lobbying), and other areas of mutual concern. Provincial MCCC offices were established from Ontario to British Columbia.

From the start its founders agreed that MCCC would work closely with MCC (International). Relations between the two organizations have generally been good, but there have been tensions from time to time. Some Canadian Mennonites have felt that MCC operated like an American rather than a bi-national institution. Several adjustments in MCC structures have been made in response to this criticism.

MCCC carries out most of its overseas relief and development work through MCC. Its own overseas programs include a ministry to the Kanadier Mennonites (those who migrated to Central and South America in the 1920s and 1940s, some of whom have since returned to Canada), relating to Mennonites in the Soviet Union, sponsoring refugees, gathering commodities such as grain, milk powder, cooking oil, etc., for shipment overseas, and administering its own Ten Thousand Villages program, under which MCCC buys handmade crafts from artisans in developing countries and sells them at a price which, although relatively inexpensive for North Americans, provides a fair wage for the artisans.

Since 1963 there has been tremendous expansion in MCCC's activities in Canada. A voluntary service program places 150 volunteers in communities across the country. A Peace and Social Concerns Committee raises awareness on peace and current social issues. A Native Concerns program promotes economic development in Native communities and engages in advocacy on behalf of Native people. An Ottawa office, established in 1974 after nine years of discussion, facilitates relations with government. A victim-offender ministry supports groups pursuing mediation and reconciliation as an alternative to the secular justice system. Since 1980, MCCC has also begun programs to address the needs of women, disabled persons, the unemployed, and the mentally ill.

In 1976 MCCC created the Mennonite Food Bank as a means of channeling surplus grains grown by Mennonite farmers into overseas use. In 1982 MCCC invited other Canadian churches to participate in this venture. The following year the Canadian Foodgrains Bank was formed, with MCCC taking its place as one of seven member church organizations.

Since 1963 MCCC has grown from a staff of two and a budget of $300,000 to a staff of 112 and a budget of $23 million in 1997. Since 1969 MCCC has received matching grants from the Canadian International Development Agency (CIDA) of the Canadian government. In 1994, government grants (CIDA and others) accounted for nearly half of MCCC's income.